The goal of this proposal is to support innovative research in functional proteomics for investigators at the University of Colorado, Boulder (CU-Boulder). Funds are requested to purchase an integrated system for shotgun proteomic profiling by multidimensional LC/MS/MS and profiling protein post-translational modifications (PTMs), building on a novel approach to more sensitive and accurate proteomic profiling, as well as new computational tools for data reduction. The system includes a ABI-4000 QTrap mass spectrometer capable of rapid scanning and high mass accuracy for efficient data collection and two HPLCs. Advantages of the requested instrument are: 1) higher quality MS/MS spectra and higher percentage of usable data generated in each file, 2) superior performance with phosphopeptide sequencing, and 3) no requirement for a large computer cluster to support data collection. The user group includes protein chemists, geneticists, cell biologists, computational scientists, and clinicians, with expertise in mass spectrometry, signal transduction, cancer biology, mammalian and microbial cell regulation, genomics, evolutionary diversity metabolic pathways, computational modeling, and databasing. The projects are highly complementary, and represent research along major themes of (1) eukaryotic signal transduction, cellular regulation, and disease progression, and (2) microbial diversity and mechanisms of host-pathogen interactions. [unreadable] [unreadable] The system will be managed by the Central Analytical Facility, which will provide technical, computational, and bioinformatics support needed for users to carry out proteomic profiling experiments. This facility provides investigators throughout the university with open access to departmental and investigator-owned instruments, and has 10 years of experience as a training facility that emphasizes handson student use, in addition to traditional service arrangements. A Facility Manager and MS Technician will be responsible for daily operation and maintenance of the system; both will be supervised by a faculty member serving as Facility Director. The cost of instrument operation, service contracts, and partial support for facility staff will be recovered through user fees. An internal advisory committee consisting of faculty users and non-users will ensure equitable distribution of instrument time and fairness in fee schedules for use of the instrument. [unreadable] [unreadable]